Changed rn3 to rn6 for a couple external links on the trait page

Made some text bold on trait page details

10 files changed, 181 insertions, 106 deletions

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index ddf6dd50..ea1ca5ed 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -146,7 +146,7 @@ class DisplayMappingResults(object):
 
         self.dataset = start_vars['dataset']
         self.this_trait = start_vars['this_trait']
-        self.n_samples = len(start_vars['vals'])
+        self.n_samples = start_vars['num_vals']
         self.species = start_vars['species']
         self.genofile_string = ""
         if 'genofile_string' in start_vars:
@@ -168,8 +168,8 @@ class DisplayMappingResults(object):
             self.mapmodel_rqtl_geno = start_vars['model']
             self.pair_scan = start_vars['pair_scan']
 
-        if self.mapping_method != "gemma" and self.mapping_method != "plink":
-            self.js_data = start_vars['js_data']
+        #if self.mapping_method != "gemma" and self.mapping_method != "plink":
+        self.js_data = start_vars['js_data']
         self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table
 
         if self.dataset.group.species == "rat":
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index b74a1c4d..809d0ce4 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -95,7 +95,8 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
                     marker['chr'] = line.split("\t")[2]
                 marker['cM'] = float(line.split("\t")[3])
                 marker['Mb'] = float(line.split("\t")[4])
-                marker['p_value'] = float(line.split("\t")[7])
+                if float(line.split("\t")[7]) != 1:
+                    marker['p_value'] = float(line.split("\t")[7])
                 marker['lrs_value'] = float(line.split("\t")[5])
                 marker['lod_score'] = marker['lrs_value'] / 4.61
                 marker['additive'] = float(line.split("\t")[6])
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 676df391..7f6bb0a5 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -85,6 +85,8 @@ class RunMapping(object):
                         self.samples.append(sample)
                         self.vals.append(value)
 
+        self.num_vals = start_vars['num_vals']
+
         #ZS: Check if genotypes exist in the DB in order to create links for markers
         if "geno_db_exists" in start_vars:
             self.geno_db_exists = start_vars['geno_db_exists']
@@ -311,14 +313,32 @@ class RunMapping(object):
 
           else:
               self.qtl_results = []
+              self.qtl_results_for_browser = []
               highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
               for marker in results:
+                  browser_marker = dict(
+                      chr = str(marker['chr']),
+                      rs  = marker['name'],
+                      ps  = marker['Mb']*1000000
+                  )
+                  if 'p_value' in marker:
+                      browser_marker['p_wald'] = marker['p_value']
+                  else:
+                      if 'lrs_value' in marker and marker['lrs_value'] > 0:
+                        browser_marker['p_wald'] = -math.log10(marker['lrs_value']/4.16)
+                      elif 'lod_score' in marker and marker['lod_score'] > 0:
+                        browser_marker['p_wald'] = -math.log10(marker['lod_score'])
+                      else:
+                        browser_marker['p_wald'] = 0
+                  self.qtl_results_for_browser.append(browser_marker)
                   if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
                       if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
                           highest_chr = marker['chr']
                       if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
                           self.qtl_results.append(marker)
 
+              browser_files = write_input_for_browser(self.dataset, self.qtl_results_for_browser)
+
               with Bench("Exporting Results"):
                   export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
 
@@ -330,50 +350,23 @@ class RunMapping(object):
                   self.trimmed_markers = trim_markers_for_table(results)
 
               if self.mapping_method != "gemma":
-                  self.json_data['chr'] = []
-                  self.json_data['pos'] = []
-                  self.json_data['lod.hk'] = []
-                  self.json_data['markernames'] = []
-
-                  self.json_data['suggestive'] = self.suggestive
-                  self.json_data['significant'] = self.significant
-
-                  #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
-                  for index, qtl in enumerate(self.qtl_results):
-                      #if index<40:
-                      #    logger.debug("lod score is:", qtl['lod_score'])
-                      if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
-                          #logger.debug("changing to X")
-                          self.json_data['chr'].append("X")
-                      else:
-                          self.json_data['chr'].append(str(qtl['chr']))
-                      self.json_data['pos'].append(qtl['Mb'])
-                      if 'lrs_value' in qtl.keys():
-                          self.json_data['lod.hk'].append(str(qtl['lrs_value']))
-                      else:
-                          self.json_data['lod.hk'].append(str(qtl['lod_score']))
-                      self.json_data['markernames'].append(qtl['name'])
-
-                  #Get chromosome lengths for drawing the interval map plot
-                  chromosome_mb_lengths = {}
-                  self.json_data['chrnames'] = []
-                  for key in self.species.chromosomes.chromosomes.keys():
-                      self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
-                      chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
-
                   self.js_data = dict(
-                      result_score_type = self.score_type,
-                      json_data = self.json_data,
-                      this_trait = self.this_trait.name,
-                      data_set = self.dataset.name,
-                      maf = self.maf,
-                      manhattan_plot = self.manhattan_plot,
-                      mapping_scale = self.mapping_scale,
-                      chromosomes = chromosome_mb_lengths,
-                      qtl_results = self.qtl_results,
+                      #result_score_type = self.score_type,
+                      #this_trait = self.this_trait.name,
+                      #data_set = self.dataset.name,
+                      #maf = self.maf,
+                      #manhattan_plot = self.manhattan_plot,
+                      #mapping_scale = self.mapping_scale,
+                      #chromosomes = chromosome_mb_lengths,
+                      #qtl_results = self.qtl_results,
                       num_perm = self.num_perm,
                       perm_results = self.perm_output,
+                      browser_files = browser_files
                   )
+              else:
+                self.js_data = dict(
+                    browser_files = browser_files
+                )
 
     def run_rqtl_plink(self):
         # os.chdir("") never do this inside a webserver!!
@@ -497,3 +490,17 @@ def trim_markers_for_table(markers):
         return trimmed_sorted_markers
     else:
         return sorted_markers
+
+def write_input_for_browser(this_dataset, markers):
+    file_base = this_dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+    gwas_filename = file_base + "_GWAS"
+    annot_filename = file_base + "_ANNOT"
+    gwas_path = "{}/gn2/".format(TEMPDIR) + gwas_filename
+    annot_path = "{}/gn2/".format(TEMPDIR) + annot_filename
+
+    with open(gwas_path + ".json", "w") as gwas_file, open(annot_path + ".json", "w") as annot_file:
+        gwas_file.write(json.dumps(markers))
+        annot_file.write(json.dumps([]))
+
+    return [gwas_filename, annot_filename]
+    #return [gwas_filename, annot_filename]
\ No newline at end of file
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 444e1f40..e74fef80 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -25,7 +25,7 @@ from db import webqtlDatabaseFunction
 
 from wqflask import user_manager
 
-from flask import render_template
+from flask import render_template, Flask, g
 
 from utility import formatting
 from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
@@ -47,6 +47,7 @@ views.py).
         ###########################################
 
         self.uc_id = uuid.uuid4()
+        self.go_term = None
         logger.debug("uc_id:", self.uc_id) # contains a unique id
 
         logger.debug("kw is:", kw)         # dict containing search terms
@@ -157,25 +158,31 @@ views.py).
             combined_where_clause = ""
             previous_from_clauses = [] #The same table can't be referenced twice in the from clause
             for i, a_search in enumerate(self.search_terms):
-                the_search = self.get_search_ob(a_search)
-                if the_search != None:
-                    get_from_clause = getattr(the_search, "get_from_clause", None)
-                    if callable(get_from_clause):
-                        from_clause = the_search.get_from_clause()
-                        if from_clause in previous_from_clauses:
-                            pass
-                        else:
-                            previous_from_clauses.append(from_clause)
-                            combined_from_clause += from_clause
-                    where_clause = the_search.get_where_clause()
-                    combined_where_clause += "(" + where_clause + ")"
-                    if (i+1) < len(self.search_terms):
-                        if self.and_or == "and":
-                            combined_where_clause += "AND"
-                        else:
-                            combined_where_clause += "OR"
+                if a_search['key'] == "GO":
+                    self.go_term = a_search['search_term'][0]
+                    gene_list = get_GO_symbols(a_search)
+                    self.search_terms += gene_list
+                    continue
                 else:
-                    self.search_term_exists = False
+                    the_search = self.get_search_ob(a_search)
+                    if the_search != None:
+                        get_from_clause = getattr(the_search, "get_from_clause", None)
+                        if callable(get_from_clause):
+                            from_clause = the_search.get_from_clause()
+                            if from_clause in previous_from_clauses:
+                                pass
+                            else:
+                                previous_from_clauses.append(from_clause)
+                                combined_from_clause += from_clause
+                        where_clause = the_search.get_where_clause()
+                        combined_where_clause += "(" + where_clause + ")"
+                        if (i+1) < len(self.search_terms):
+                            if self.and_or == "and":
+                                combined_where_clause += "AND"
+                            else:
+                                combined_where_clause += "OR"
+                    else:
+                        self.search_term_exists = False
             if self.search_term_exists:
                 combined_where_clause = "(" + combined_where_clause + ")"
                 final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause)
@@ -186,11 +193,19 @@ views.py).
                 self.search_term_exists = False
             else:
                 for a_search in self.search_terms:
-                    the_search = self.get_search_ob(a_search)
-                    if the_search != None:
-                        self.results.extend(the_search.run())
+                    logger.debug("TERMS:", self.search_terms)
+                    if a_search['key'] == "GO":
+                        self.go_term = a_search['search_term'][0]
+                        gene_list = get_GO_symbols(a_search)
+                        self.search_terms += gene_list
+                        self.search_terms.pop(0)
+                        continue
                     else:
-                        self.search_term_exists = False
+                        the_search = self.get_search_ob(a_search)
+                        if the_search != None:
+                            self.results.extend(the_search.run())
+                        else:
+                            self.search_term_exists = False
 
         if self.search_term_exists:
             if the_search != None:
@@ -218,9 +233,27 @@ views.py).
         else:
             return None
 
+def get_GO_symbols(a_search):
+    query = """SELECT genes
+               FROM GORef
+               WHERE goterm='{0}:{1}'""".format(a_search['key'], a_search['search_term'][0])
+
+    gene_list = g.db.execute(query).fetchone()[0].strip().split()
+
+    new_terms = []
+    for gene in gene_list:
+        this_term = dict(key=None,
+                         separator=None,
+                         search_term=[gene])
+
+        new_terms.append(this_term)
+
+    return new_terms
+
 def insert_newlines(string, every=64):
     """ This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """
     lines = []
     for i in xrange(0, len(string), every):
         lines.append(string[i:i+every])
     return '\n'.join(lines)
+
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index f1f5840f..b0a46b32 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -107,7 +107,7 @@ class ShowTrait(object):
                     blatsequence += '%3EProbe_' + string.strip(seqt[1]) + '%0A' + string.strip(seqt[0]) + '%0A'
 
             if self.dataset.group.species == "rat":
-                self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence)
+                self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn6', blatsequence)
                 self.UTHSC_BLAT_URL = ""
             elif self.dataset.group.species == "mouse":
                 self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm10', blatsequence)
@@ -314,7 +314,7 @@ class ShowTrait(object):
                 if chr and transcript_start and transcript_end and kgId:
                     transcript_start = int(transcript_start*1000000) # Convert to bases from megabases
                     transcript_end = int(transcript_end*1000000)
-                    self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('rn3', kgId, chr, transcript_start, transcript_end)
+                    self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('rn6', kgId, chr, transcript_start, transcript_end)
 
             if self.this_trait.geneid and (self.dataset.group.species == "mouse" or self.dataset.group.species == "rat" or self.dataset.group.species == "human"):
                 self.biogps_link = webqtlConfig.BIOGPS_URL % (self.dataset.group.species, self.this_trait.geneid)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 48b6da5e..53158885 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -940,6 +940,7 @@ if (js_data.num_values < 256) {
   root.bar_layout = {
     title: js_data.trait_id,
     xaxis: {
+        type: 'category',
         titlefont: {
           size: 16
         },
@@ -947,7 +948,7 @@ if (js_data.num_values < 256) {
         ticklen: 4,
         tickfont: {
           size: 16
-        }
+        },
     },
     yaxis: {
         title: js_data.unit_type,
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 98931166..b8b64761 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -3,9 +3,11 @@
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+    <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous">
+    <link rel="stylesheet" type="text/css" href="/static/packages/purescript_genome_browser/css/purescript_genetics_browser_v01.css" />
 
     <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
+
 {% endblock %}
 {% from "base_macro.html" import header %}
 {% block content %}
@@ -29,6 +31,7 @@
         {% for sample in samples %}
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
         {% endfor %}
+        <input type="hidden" name="num_vals" value="{{ n_samples }}">
         <input type="hidden" name="maf">
         <input type="hidden" name="use_loco" value="{{ use_loco }}">
         <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
@@ -153,11 +156,9 @@
             <li id="gn1_map_tab">
               <a href="#gn1_map" data-toggle="tab" aria-expanded="true">GN1 Map</a>
             </li>
-            {% if mapping_method != "gemma" and mapping_method != "plink" %}
-            <li id="vector_map_tab">
-              <a href="#vector_map" data-toggle="tab" {% if mapping_method != "gemma" and mapping_method != "plink" %}aria-expanded="false"{% else %}aria-expanded="true"{% endif %}>Vector Map</a>
+            <li id="browser_tab">
+                <a href="#browser_holder" data-toggle="tab" aria-expanded="true">Genome Browser</a>
             </li>
-            {% endif %}
           </ul>
           <div class="tab-content">
             <div class="tab-pane active" id="gn1_map">
@@ -177,19 +178,31 @@
                   {% endif %}
               </div>
             </div>
-            {% if mapping_method != "gemma" and mapping_method != "plink" %}
-            <div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map">
-              <div id="chart_container">
-                <div class="qtlcharts" id="topchart"></div>
-              </div>
+            <div class="tab-pane" id="browser_holder" style="height: 500px;">
+                <div id="browser">
+                    <div id="controls">
+                        <button id="scrollLeft"  type="button" >
+                          <i class="fas fa-arrow-left"></i>
+                        </button>
+                        <button id="scrollRight" type="button" >
+                          <i class="fas fa-arrow-right"></i>
+                        </button>
+                        <button id="zoomOut" type="button" >
+                          <i class="fas fa-search-minus"></i>
+                        </button>
+                        <button id="zoomIn"  type="button" >
+                          <i class="fas fa-search-plus"></i>
+                        </button>
+                        <button id="reset"  type="button" >Reset</button>
+                    </div>
+                </div>
             </div>
-            {% endif %}
           </div>
         </div>
 
         </form>
         {% if selectedChr == -1 %}
-        <div class="container" style="padding-left: 30px;">
+        <div class="container" style="padding-left: 30px; margin-top: 50px; position: relative;">
           <h2>Mapping Statistics</h2>
         <br />
         <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
@@ -307,20 +320,14 @@
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/purescript_genome_browser/js/purescript-genetics-browser_v01.js"></script>
 
-    {% if mapping_method != "gemma" and mapping_method != "plink" %}
     <script>
         js_data = {{ js_data | safe }}
     </script>
-    {% endif %}
 
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
-    {% if mapping_method != "gemma" and mapping_method != "plink" %}
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> 
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
-    {% endif %}
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/init_genome_browser.js"></script>
 
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
@@ -332,7 +339,8 @@
                     { "type": "natural", "width": "8%" },
                     { "type": "natural", "width": "25%" },
                     { "type": "natural" },
-                    { "type": "natural", "width": "8%" },
+                    { "type": "natural" },
+                    { "type": "natural" },
                     { "type": "natural" }{% if 'additive' in marker %},
                     { "type": "natural" }{% endif %}{% if 'dominance' in marker and dataset.group.genetic_type != "riset" %},
                     { "type": "natural" }{% endif %}
@@ -438,6 +446,12 @@
             return $('#marker_regression_form').submit();
         }
 
+        $('#browser_tab').click(function() {
+          $('#gn1_map_options').css("display", "none")
+        })
+        $('#gn1_map_tab').click(function() {
+          $('#gn1_map_options').css("display", "block")
+        })
     </script>
 
 {% endblock %}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 2dded69f..8dfa37a8 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -15,6 +15,9 @@
         <!-- Need to customize text more for other types of searches -->
         <p><b>Search Results:</b> We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
            to find all records
+                {% if go_term is not none %}
+                with <u>Gene Ontology ID</u> <strong>GO:{{ go_term }}</strong>.
+                {% else %}
                 {% for word in search_terms %}
                     {% if word.key|lower == "rif" %}
                     with <u>GeneRIF</u> containing <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
@@ -40,9 +43,13 @@
                     {% if word.search_term[0] == "*" %} in the dataset.{% else %}{% if loop.first %}that match:<br>{% endif %}<b>"{{ word.search_term[0] }}"</b>{% if loop.last %}{% else %} and {% endif %}{% endif %}
                     {% endif %}
                 {% endfor %}
+                {% endif %}
                 <br>
                 {{ results|count }} records are shown below.
         </p>
+        {% if go_term is not none %}
+        <p><b>The associated genes include:</b><br><br>{% for word in search_terms %}{{ word.search_term[0] }}{% endfor %}</p>
+        {% endif %}
 
         <!--<p>To study a record click on its ID below, and to view the whole description {% if dataset.type == "Publish" %}or list of authors {% endif %} hover over the table cell. Check records below and click Add button to add to selection.</p>-->
 
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 7714a1ab..bb0b62fe 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -1,40 +1,40 @@
 <table class="table">
     <tr>
-        <td width="150px">Species and Group</td>
+        <td width="150px"><b>Species and Group</b></td>
         <td>{{ this_trait.dataset.group.species }}, {{ this_trait.dataset.group.name }}</td>
     </tr>
     {% if this_trait.dataset.type == 'Publish' %}
     <tr>
-        <td>Phenotype</td>
+        <td><b>Phenotype</b></td>
         <td><div style="width:40%;">{{ this_trait.description_fmt }}</div></td>
     </tr>
     <tr>
-        <td>Authors</td>
+        <td><b>Authors</b></td>
         <td><div style="width:40%;">{{ this_trait.authors }}</div></td>
     </tr>
     <tr>
-        <td>Title</td>
+        <td><b>Title</b></td>
         <td><div style="width:40%;">{{ this_trait.title }}</div></td>
     </tr>
     <tr>
-        <td>Journal</td>
+        <td><b>Journal</b></td>
         <td>{{ this_trait.journal }} ({% if this_trait.pubmed_id %}<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" target="_blank" title="PubMed">{{ this_trait.year }}</a>{% else %}{{ this_trait.year }}{% endif %})</td>
     </tr>
     {% else %}
     <tr>
-        <td>Tissue</td>
+        <td><b>Tissue</b></td>
         <td>{{ this_trait.dataset.tissue }}</td>
     </tr>
     {% endif %}
     {% if this_trait.dataset.type == 'ProbeSet' %}
     {% if this_trait.symbol != None %}
     <tr>
-        <td>Gene Symbol</td>
+        <td><b>Gene Symbol</b></td>
         <td>{{ this_trait.symbol }}</td>
     </tr>
     {% endif %}
     <tr>
-        <td>Aliases</td>
+        <td><b>Aliases</b></td>
         <td>Wikidata: {{ this_trait.wikidata_alias_fmt|replace(",",";") }}</td>
     </tr>
     {% if this_trait.alias_fmt != "Not Available" %}
@@ -46,12 +46,12 @@
     {% endif %}
     {% if this_trait.dataset.type != 'Publish' %}
     <tr>
-        <td>Location</td>
+        <td><b>Location</b></td>
         <td>{{ this_trait.location_fmt }}</td>
     </tr>
     {% endif %}
     <tr>
-        <td>Database</td>
+        <td><b>Database</b></td>
         <td>
             <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName={{ dataset.name }}" target="_blank">
                 {{ dataset.fullname }}
@@ -60,7 +60,7 @@
     </tr>
     {% if this_trait.probe_set_specificity %}
     <tr>
-        <td>Target Score</td>
+        <td><b>Target Score</b></td>
         <td>
             <a href="http://genenetwork.org/blatInfo.html" target="_blank" title="Values higher than 2 for the specificity are good">
                 BLAT Specificity
@@ -75,7 +75,7 @@
     {% endif %}
     {% if this_trait.pubmed_id or this_trait.geneid or this_trait.omim or this_trait.symbol %}
     <tr>
-        <td>Resource Links</td>
+        <td><b>Resource Links</b></td>
         <td>
             {% if pubmed_link %}
             <a href="{{ pubmed_link }}" target="_blank" title="PubMed">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 7b585b03..aa64a910 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -639,7 +639,8 @@ def mapping_results_page():
         'mapmethod_rqtl_geno',
         'mapmodel_rqtl_geno',
         'temp_trait',
-        'reaper_version'
+        'reaper_version',
+        'num_vals'
     )
     start_vars = {}
     for key, value in initial_start_vars.iteritems():
@@ -670,8 +671,8 @@ def mapping_results_page():
         if template_vars.no_results:
             rendered_template = render_template("mapping_error.html")
         else:
-          if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
-              template_vars.js_data = json.dumps(template_vars.js_data,
+          #if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
+          template_vars.js_data = json.dumps(template_vars.js_data,
                                                  default=json_default_handler,
                                                  indent="   ")
 
@@ -808,6 +809,17 @@ def get_temp_data():
     temp_uuid = request.args['key']
     return flask.jsonify(temp_data.TempData(temp_uuid).get_all())
 
+@app.route("/browser_input", methods=('GET',))
+def browser_inputs():
+    """  Returns JSON from tmp directory for the purescript genome browser"""
+
+    filename = request.args['filename']
+
+    with open("{}/gn2/".format(TEMPDIR) + filename + ".json", "r") as the_file:
+        file_contents = json.load(the_file)
+
+    return flask.jsonify(file_contents)
+
 ##########################################################################
 
 def json_default_handler(obj):